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f4b7cd4908b99f346c86b242d3047ef816fe84d3bb2f1ad3a50981a240067c3c | Text | 7,223 | 133 |
The source code of paper 'Whole Brain Alignment of Spatial Transcriptomics between Humans and Mice with BrainAlign'
# BrainAlign
[](https://opensource.org/lice... |
9f57ee0cc490b9352623341c292213324a3d65c1c30ebac48edc6d5a747dd32b | Text | 7,243 | 97 | # cross_modal_task
This repository contains methods to analyze single-neuron activity, neural population activity, and animal behaviors in a cross-modal sensory selection task. The findings are shown in Chang Yi-Ting, Finkel Eric A., Xu Duo, O’Connor Daniel H. (2023) Rule-based modulation of a sensorimotor transformati... |
f389b4bb8ddf905df5f5c251dc44ccff69f65ee28e518312a4bd9899ff4c276d | Text | 7,251 | 103 | # Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC)
<p float="left">
<img src="https://raw.githubusercontent.com/MRN-Code/coinstac/master/img/coinstac.png" height="75px">
</p>
[](https://circleci.c... |
cedc8d5ef5fe3e5cdfb4b59207674fdad13cb09a153e864507710433b7985951 | Text | 7,275 | 206 | # Mantis-ML 2.0
- [Introduction](#introduction)
- [Installation](#installation)
- [Run](#run)
Introduction
============
We previously introduced Mantis-ML, an automated machine-learning framework able to generalize from a set of known associated genes, identifying disease-gene association levels exome-wide base... |
f04e648950ac8bbc57d7ac18b30cba6ebeee7e42370e7f266b66905d9eb79229 | Text | 7,286 | 195 |
[](https://dev.azure.com/3decision/fpocket/_build/latest?definitionId=2&branchName=master)
[ from 19k human protein-coding genes (canonical transcripts) for both hg19 and hg38 coordinates. These files are sorted by genomic coordinates.
### AlphaM... |
5d6f7b8eab201dc8bc56421ab40dc3dffdaeff9d892813e1907f894601bc4eae | Text | 7,599 | 120 | # MuTILs: explainable, multiresolution panoptic segmentation of the breast tumor microenvironment
## Paper
Access [here](https://www.nature.com/articles/s41523-024-00663-1). Citation:
```
Shangke Liu, Mohamed Amgad, Deeptej More, Muhammad A. Rathore, Roberto Salgado, Lee A. D. Cooper: A panoptic segmentation dataset a... |
d42f66e0fb120545c38a0ee83fdf4c2a9760317434030175595c430ef65d93a1 | Text | 7,609 | 240 | # Neurotransmitter Prediction from Electron Microscopy Images in Drosophila Melanogaster
This repository accompanies the preprint [Neurotransmitter Classification from
Electron Microscopy Images at Synaptic Sites in
Drosophila.](https://www.biorxiv.org/content/10.1101/2020.06.12.148775v2)
## Access to Neurotransmitte... |
ca327ea86cd4e66c860311781043f32d279808bb1371d39d2d50dd6e2b28bfeb | Text | 7,653 | 103 | # HuMMuS <img src="man/figures/hummus_logo.png" align="right" width="180"/>
[](https://github.com/cantinilab/HuMMuS/a... |
af3fc3aa92b20a70ea0753615f06318d9fafd63e4b022af168c5005a89c3b985 | Text | 7,733 | 178 | Using the DADA2 pipeline for sequence variant identification
============================================================
Here we provide a R Notebook template to generate a sequences variants table from FASTQ files generated by Paired-End Illumina sequencing. For maximal reproducibility, we also provide a R project f... |
e722147c1017c8516c1f9e39dea31be204175630ec765a191890e0ac8708809b | Text | 7,799 | 183 | # Pytorch Implementation of PointNet and PointNet++
This repo is implementation for [PointNet](http://openaccess.thecvf.com/content_cvpr_2017/papers/Qi_PointNet_Deep_Learning_CVPR_2017_paper.pdf) and [PointNet++](http://papers.nips.cc/paper/7095-pointnet-deep-hierarchical-feature-learning-on-point-sets-in-a-metric-sp... |
772adb652f4022a6eb6e934d49d05b9ec138fa77b3725dbb9006806cb482e30b | Text | 7,889 | 54 | [](https://github.com/xihaoli/STAAR/actions)
[](https://ci.appveyor.com/project/xihaoli/STAAR)
[ by Guanglei Yu, Qichang Zhao, Xuehua Bi and Jianxin Wang.
We proposed a [ProteinMPNN](https:... |
3e9267eacb22f28c105844dc08dfd105e8313c7a267aafd88af95d0214a2d666 | Text | 8,108 | 229 | ## Literature Info
For detailed model benchmarking and architecture introduction, please see the publication: [TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation](https://academic.oup.com/bib/article/25/4/bbae308/7699353)
## Environments
#### To avoid potent... |
669c84c74ccd2155180de7995df881b6ba7372ad4f1341d518c6d5870e43ad8f | Text | 8,431 | 184 | # Pipeline for creating SNP-weights for TWAS using FUSION
This pipeline is to create SNP-weights that can be used in TWAS using FUSION. I provide a series of R scripts to process the input and output files for the FUSION script called 'FUSION.compute_weights.R'. I also provide all the software and data required for t... |
e60bee9fc491db1d0e76b8661c7a7c78f34d34d2b65a3fbc4dd2d154cf5eca2a | Text | 8,535 | 147 | <p align="center">
<img src="https://raw.githubusercontent.com/TissueImageAnalytics/tiatoolbox/develop/docs/tiatoolbox-logo.png">
</p>
<h1 align="center">TIA Toolbox</h1>
<h3 align="center">Computational Pathology Toolbox developed at the TIA Centre</h3>
<a href="https://badge.fury.io/py/tiatoolbox">
<img src="h... |
00a70018864cd01f873ce728a5b766cbc148aa7811e8e8e8b308dd4ff2b6d856 | Text | 8,685 | 167 | ## Detecting CNN-Generated Images [[Project Page]](https://peterwang512.github.io/CNNDetection/)
**CNN-generated images are surprisingly easy to spot...for now**
[Sheng-Yu Wang](https://peterwang512.github.io/), [Oliver Wang](http://www.oliverwang.info/), [Richard Zhang](https://richzhang.github.io/), [Andrew Owens]... |
3b8c9f0213f844b95446edd6eb4e7ec69d2e15b73adeb355527c02136de01e8e | Text | 8,692 | 193 | # Protein sequence design with a learned potential
Code for the algorithm in our paper
> Namrata Anand-Achim, Raphael R. Eguchi, Alexander Derry, Russ B. Altman, and Possu Huang. "Protein sequence design with a learned potential." bioRxiv (2020).
> [[biorxiv]](https://www.biorxiv.org/content/10.1101/2020.01.06.89546... |
f7f1a38eaac1e44e37dfa90fa5afd470be53651648a90d73ca446fe2db2707bc | Text | 8,699 | 128 | # TA-RNN & TA-RNN-AE: an Attention-based Time-aware Recurrent Neural Network Architecture for Electronic Health Record
Time-Aware RNN (TA-RNN) and TA-RNN-Autoencoder (TA-RNN-AE) are two deep learning architectures for early predicting of clinical outcomes in Electronic Health Record (EHR) at the next visit and multiple... |
926eac3a7c4fbc4204c1b85556800e264ff802e774a371a69247b1952bcc67c1 | Text | 8,757 | 203 | # Local CSF Correction Pipeline for fMRI
A modular pipeline for correcting CSF-related artifacts in subcortical fMRI to improve signal sensitivity and reduce physiological confounds in ultra-high field (7T) imaging.
---
## Purpose
Subcortical regions are vulnerable ... |
268f684adb8226e888fc31005f2e1b4eec580346bde813f508b8051c957e56ad | Text | 8,851 | 139 | <p align="center"><img width="25%" src="docs/logo.png"/></p>
A Python package used for simulating spiking neural networks (SNNs) on CPUs or GPUs using [PyTorch](http://pytorch.org/) `Tensor` functionality.
BindsNET is a spiking neural network simulation library geared towards the development of biologically inspired ... |
bf23def80056434563cebbd336a2a5c37abef0ad94a799902b38d3bd226971c9 | Text | 8,898 | 121 | [](https://opensource.org/licenses/MIT)
[](https://www.frontiersin.org/articles/10.3389/fmed.2021.816281/full)
[]([https://yo... |
cbe1f3b1f064417723b5021a00a7f0391e1013514a8a71e46a8aedbd0a7640bc | Text | 8,920 | 267 | # Category-wide association study (CWAS)
**CWAS (Category-Wide Association Study)** is a data analytic tool to perform stringent association tests to find non-coding loci associated with autism spectrum disorder (ASD). CWAS run... |
7e059584d3b2e427ee9a23dd54e7cff6ac89c179947f2e6b1e537f574a181e8b | Text | 8,997 | 106 | # Monkey behavioral neurophysiology during a delayed center-out reach task with ambiguous target information.
This data set contains behavioral and neurophysiological data obtained in two behaving monkeys. The experimental task involves a delayed center-out arm-reach in three experimental conditions that varied the de... |
c135ac359542d24960dcc17e5a7ee0467e4cf6d39542de841aa2214e59f3f0f9 | Text | 9,001 | 205 | ## Overview
This code provides various models combining dilated convolutions with residual networks. Our models can achieve better performance with less parameters than ResNet on [image classification](#image-classification) and [semantic segmentation](#semantic-image-segmentataion).
If you find this code useful for ... |
ff078c69e7784efcd2b9f2b98cb29eda7e654e9e404df782444dd806a6fe819f | Text | 9,026 | 128 | <br>
# cuda_voxelizer v0.6
A command-line tool to convert polygon meshes to (annotated) voxel grids.
* Supported input formats: .ply, .off, .obj, .3DS, .SM and RAY
* Supported output formats: .vox, .binvox, .obj cubes and point clou... |
ab2f8b4ed3b54d2004f18c139cc36f150cae9ec7d496bc439527d9c38676ad97 | Text | 9,098 | 92 |
## Retro-MoCo-Box
Matlab toolbox for retrospective motion-correction of 3D MRI k-space data - as used for my work using 3D FatNavs to obtain the motion information. You can read more... |
efffd96d1737b3ec39608165756ba5d7be54293462376d2bb1a2706abc535181 | Text | 9,129 | 126 | ## Table of Contents
1. [Introduction](#introduction)
2. [Prerequisites](#prerequisites)
3. [Usage](#usage)
4. [Inputs and pre-processing](#inputs-and-pre-processing)
5. [Outputs](#outputs)
<a name="introduction"/>
# Introduction
MutSpace is a method aiming to address the computational challenge to consider large-s... |
b4f0f86d2c32758d7d94e387d3b1ea5ad3392869cf1bd88c9c99348a44aaf796 | Text | 9,138 | 84 | [DOI] -
[Title] Supporting data for SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations
[Release Date] 2023-11-6
[Data Type] raw and processed data
[Dataset Summary] Drug combination synergy data along with other external bioinformatic datasets used t... |
7f55fc6b9393fac2fb7f2ae8551546cfa40e4aa333194d19a647bf6797f48101 | Text | 9,235 | 64 | The Lateral Amygdala Network dataset
The raw data in this dataset concern analyses of synaptic connections between glutamatergic neurons in the lateral nucleus of the amygdala (LA), and how these connections encode fear memory through local synaptic plasticity. The dataset consists of in vitro, ex vivo and in vivo e... |
73fb2377d87773af8dd24326c7ae4c138ab8ba04f938511fec2cd9e3028f3701 | Text | 9,300 | 92 | | **Status** | [](https://github.com/openforcefield/openff-toolkit/actions?query=branch%3Amain+workflow%3ACI) [
<p align="justify">
Clust3D is a clustering tool designed for clustering 3D data, such as timeseries and multi-omic datasets, using a self-adjusting neural network.
Clust3D provides the capability to directly cluster 3D data, exploiting the entire data structure, without the need ... |
97648c27001b18a1ab78996c44be1729797ba4ca019f1709b3f6740f438882f7 | Text | 9,332 | 241 | Install using Docker
====================
If you don't want to do the compilation yourself and just want to quickly try STEPS, we provide a prebuilt Docker image for you. Please check https://github.com/CNS-OIST/STEPS_Docker and follow the instructions.
Install from source code
========================
To facilitate ... |
3e935af9f21ed3f5094b8879e32b4fda235d62a442afa5c4690b6dcb7a747d61 | Text | 9,453 | 238 | # Placebo Intervention Enhances Reward Learning in Healthy Individuals
[](https://zenodo.org/badge/latestdoi/19634/ihrke/2016-placebo-tdcs-study)
This repository contains data and analyses for the paper "Placebo Intervention Enhances Reward Learn... |
2347176255a8e0778a828777b97a9caa5f72e14e4a67a19eef8ee21dc070e7ab | Text | 9,536 | 189 | About
-----
Source code of the paper [Deep learning for precipitation nowcasting: A benchmark and a new model](http://papers.nips.cc/paper/7145-deep-learning-for-precipitation-nowcasting-a-benchmark-and-a-new-model)
If you use the code or find it helpful, please cite the following paper:
```
@inproceedings{xingjian20... |
8da92d4d3eb392cee093ec9227b4d9d5aff49a8e0a0a7c1f4c8065dec871c035 | Text | 9,801 | 197 | # Spatial-Perturbation-Framework
## Table of Contents
* [Folders](#folders)
* [Prerequisites](#prerequisites)
* [Installation](#installation)
* [Expected runtime](#expected-runtime)
* [Getting started](#getting-started)
* [Running the SP framework on your own data](#running-the-SP-framework-on-your... |
764848cd0810d401846d089c7f868820ece521bc314661baaeffaac86b7bfd09 | Text | 9,918 | 194 | Ada-Learn
=========
This repository accompanies the paper:
> **Two determinants of dynamic adaptive learning for magnitudes and probabilities**
> Cédric Foucault, and Florent Meyniel
> *Open Mind: Discoveries in Cognitive Science (2024)*
Link to the article: [doi.org/10.1162/opmi_a_00139](https://doi.org/10.1... |
f8b5ec93be0ec5d78d9ac80dbe090d28a773e752f79f852654645431ddb92ad6 | Text | 9,919 | 126 | # DyMINSTED4all
Open source instructions and code for making your STED microscope a Dymin STED
## Description
Using inexpensive parts and labview code, we implemented DyMIN STED Microscopy as detailed from in the paper: [Adaptive Illumination STED Nanoscopy](https://www.pnas.org/content/114/37/9797). The following fi... |
885c97e6da7e7b743007ba7277eb166a834624b00012c8f14bf8bf8878b365bc | Text | 9,940 | 264 | <!-- README.md is generated from README.Rmd. Please edit that file -->
# mice <a href="https://amices.org/mice/"><img src="man/figures/logo.png" align="right" height="139" /></a>
<!-- badges: start -->
[](https://cran.r-project.org/package=mice)
[](https://zenodo.org/doi/10.5281/zenodo.10838383)
[](https://zenodo.org/doi/10.5281/zenodo.10838431)
[](https://doi.or... |
70279f182e8747444922baa428f612f582ce0ff26a171dab71a67c7d3ef63f73 | Text | 10,094 | 202 | Atlas of Lateralized visuospatial Attentional Networks (ALANs)
================
[](https://doi.org/10.5281/zenodo.10655105)
------------------------------------------------------------------------
In accordance with the
[SENSAAS](https://github.com/loic... |
90feff5f387b1391fd0023196732546b92f964672eaba83e1933dcae6442fde2 | Text | 10,192 | 174 | # Simple Impedance Analyzer
## Purpose
The impedance analyzer was designed as a low-cost, flexible, and accurate platform to perform impedance measurement at arbitrary frequencies up to ~250kHz. The current infrastructure assumes the user has access to a National Instruments DAQ (e.g. NI-USB-6363), though similar dig... |
5f3b9a001754ab805ceeec50bd3fda53be19e61c7312a41ccf13e0ad4e6db565 | Text | 10,220 | 231 | <p align="center">
<img src="https://github.com/user-attachments/assets/00367e51-0e0a-445e-8d12-2a273f9014aa" alt="Image" width="50%">
</p>
[](https://pypi.org/project/waveorder)
[![PyPI monthly downloads](https://img.shields.io/pypi/dm/waveorder.sv... |
fde7624a2b9dc65a344549e939212c5814858c44502f108ce79ad36503aad8e7 | Text | 10,310 | 222 | <p align="center">
<img alt="nerfstudio" src="media/sdf_studio_4.png" width="300">
<h1 align="center">A Unified Framework for Surface Reconstruction</h1>
<h3 align="center"><a href="https://autonomousvision.github.io/sdfstudio/">Project Page</a> | <a href="docs/sdfstudio-methods.md">Documentation</a> | <a h... |
921d000b42e3a4027072888508e7162dabd74977168ad0ffe96b3c2064cf3b4e | Text | 10,377 | 246 | # Drop-Width Estimation from Side-View Videos
<p align="center">
<img src="The setup.png" alt="experimental setup" width="65%">
</p>
A Python toolkit to estimate the **front-view width** of a liquid drop sliding down an inclined surface using only **side-view** measurements.\
Implementation of Shumaly *et al.*, *... |
cfb296e594994b6a9fb72f0372c557b9ddf26c186e40b88a331f27426980da9f | Text | 10,636 | 165 | # Local CSF Correction Pipeline for fMRI
[](https://doi.org/10.5281/zenodo.15236635)  [](https://opensource.org/licenses/M... |
bb835a15d5b873b29ef4f8b48b6d5504ec902da05257661d92ee5c4224fbf57c | Text | 10,695 | 242 | # GENIE
**G**ene-**EN**viroment **I**nteraction **E**stimator
## Prerequisites
The following packages are required on a Linux machine to compile and use the software package.
```
g++
cmake
make
```
## How to install :
```
git clone https://github.com/sriramlab/GENIE.git
cd GENIE
mkdir build
cd build/
cmake ..
make
`... |
162266295879461fade2b8c6403d0b0dc0c09e5cd6ca41c91bb2671c69ef2891 | Text | 10,809 | 314 | # FermiNet: Fermionic Neural Networks
FermiNet is a neural network for learning highly accurate ground state
wavefunctions of atoms and molecules using a variational Monte Carlo approach.
This repository contains an implementation of the algorithm and experiments
first described in "Ab-Initio Solution of the Many-Ele... |
74804892740a05319ad5c443f953d744c52d5e84f822d73742fdc1794b62bc1e | Text | 10,884 | 235 | # M/EEG brain age prediction benchmark paper
This repository presents the code, tools and resources developed in the course of [1]. To reuse the code, please follow the instructions and recommendations below. When publishing results based on this code, please cite [1]
[1] D. Engemann, A. Mellot, R. Höchenberger, H. B... |
f526a46882c1684f6e2b82a559f22c795cf9d984e3ef0f54a923272e8edf6a14 | Text | 10,935 | 284 | # Alpaca Use Case
Repository containing the code necessary to reproduce the results of the
Alpaca toolbox manuscript.
## Table of contents
- [Prerequisites](#prerequisites)
- [Installation](#installation)
- [Code repository](#code-repository)
- [How to run](#how-to-run)
- [Outputs](#outputs)
- [Acknowle... |
0af036c1d02b150f6402a53960a6e995611e66ee7724b61a21f58d3366ec8eda | Text | 11,092 | 171 | Papyrus README file
===================
last modified: Aug. 25, 2022
Papyrus version: 5.5
Total number of files: 14
===================
Papyrus is an aggregated dataset of small molecule bioactivities.
The very high quality Papyrus++ data in contained in the
05.5++_combined_set_without_stereochemistry.... |
cdf4a7f070e818fbaa5e1e8c1a7aae50216874dcd3fd22470deaedcb546813e4 | Text | 11,335 | 237 | # GFPPeaks
The MATLAB script in this repository enable the semi-automatic identification of [Global Field Power (GFP)](https://www.hindawi.com/journals/cin/2011/813870/) peaks on Event-Related Potentials (ERP) files.
The method is based on: [Wicht, C.A., De Pretto, M. & Spierer L.; Neural correlates of expectations-... |
4622ac886c932d52934661ecef8cf0a388c6e29c4a59f21ef55bee0ba14c6a35 | Text | 11,343 | 225 | # REACT: Receptor-Enriched Analysis of functional Connectivity by Targets
[](https://zenodo.org/badge/latestdoi/362894234)
The `react-fmri` softwa... |
625c49e7dedf84826b350be28d118e7823e669504689105611e91ff709406d1f | Text | 11,598 | 223 | # 🗂️ LlamaIndex Framework 🦙
[](https://pypi.org/project/llama-index/)
[](https://github.com/run-llama/llama_index/actions/workflows/build_package.yml)
[. For example:
```
python -m venv stepsenv
source stepsenv/bin/activate
```
Once the environment is activated, you can install STEPS from PyPI or from the source... |
6c18df4cd8c420b2280f8c55699c87baf8269f8170ea588b04b91e909bf17a28 | Text | 11,851 | 240 | # Comparative Markov State Analysis (CoVAMPnet)
Code supplementing the paper "CoVAMPnet: comparative Markov state analysis for studying effects of drug candidates on disordered biomolecules" [published in JACS Au](https://pubs.acs.org/doi/full/10.1021/jacsau.4c00182).
For training the VAMPnet and for performing the a... |
d7171a90444e05a774dae4202c5ea9e9b2835d8f6b74ed8102a8cb38e158b854 | Text | 11,857 | 144 | # Macaque Cage Query Extension (MaCaQuE)
MaCaQuE is a visuo-haptic interaction system for unrestrained rhesus monkeys that allows training the animals to goal-directed movement tasks within a cage. The system was developed for sensorimotor neuroscience and tested within the Reach Cage experimental environment:
> Berg... |
fae26d3cadd6d570967419de27150d16bfbd1d8684bb1b71d4bccb7918de7c63 | Text | 12,084 | 131 | # Tool recommender system in Galaxy using deep learning (Gated recurrent units neural network)
## Published article: https://doi.org/10.1093/gigascience/giaa152
[](https://zenodo.org/badge/latestdoi/241409061) [ is a software which was written to analyze the structure of the osteocyte lacuno canalicular networks (OLCN) in osteons. The work was concluded during my PhD at the [MPIKG](http://www.mpikg.mpg.de/).
The following scientific publicat... |
e7b9760e1e32b9ea705f1c9d55fa5a5815a49e25b473db69833baef694fde554 | Text | 12,177 | 151 | [](https://zenodo.org/badge/latestdoi/139443863)
# Macaque Cage Query Extension (MaCaQuE)
MaCaQuE is a visuo-haptic interaction system for unrestrained rhesus monkeys that allows training the animals to goal-directed movement tasks within a cage. The system was developed... |
b4ebed107473045242d4709eebad9368449f5c7ac62c3c83895c786fdb54fe8c | Text | 12,355 | 186 | # SPM UP
SPM utlities plus are tools designed to get the best of mass univariate analyses.
## Installation
This acts as a toolbox - place it in /spm12/toolbox/ and run spmup.m which will add all the other paths, copy gp_event_plot.m to appear in the spm toolbox tab, and save this.
## Pipeline
There is an automated... |
8a75713e86f2a16fa083ce8ab4bc455a4d285bde67afecb2f0cd6decd81d4361 | Text | 12,728 | 213 | [](https://zenodo.org/badge/latestdoi/476440894)
# SpaceFlow: Identifying Multicellular Spatiotemporal Organization of Cells using Spatial Transcriptome Data
SpaceFlow is Python package for identifying spatiotemporal patterns and spatial domains from Spatial Transcriptomi... |
44c9e2c8d5b336aa389ab5619bb3a2c6d9849f387fe720ca615078ddbccd8790 | Text | 12,835 | 235 | # Graph 5hmC Convolutional Network (GhmCN)
<img src="./utils/model_representation_updated.png" s=400>
<details>
<summary>To Dos</summary>
- ~~Bash script to integrate rna-seq into rnaseq.csv registry~~
- ~~child issue: add Rscript that TPM-normalizes~~
- ~~Add example data from feature counts~~
- ~~Add e... |
2a01383f217b3c8dc6e6e1c460165fe90652f1a7eb4bb30c6302a13cb93ca8b5 | Text | 12,839 | 239 | # Graph 5hmC Convolutional Network (GhmCN)
<img src="./utils/model_representation_updated.png" s=400>
<details>
<summary>To Dos</summary>
- ~~Bash script to integrate rna-seq into rnaseq.csv registry~~
- ~~child issue: add Rscript that TPM-normalizes~~
- ~~Add example data from feature counts~~
- ~~Add e... |
5ab21aacc0b0c82eecdacd2a12ef67ac152f0e5d80d614601227ac958d1dc7f9 | Text | 12,881 | 137 | # Comparative microelectrode array dataset of functional development of human pluripotent stem cell-derived and rat neuronal networks
## Authors
Fikret Emre Kapucu, Andrey Vinogradov, Tanja Hyvärinen, Laura Ylä-Outinen, Susanna Narkilahti
Neuro Group, Faculty of Medicine and Health Technology, Tampere University
##... |
b07823f92f66cba176227d512c3d6d68aa60d2b0fa6f86cabb403e69ca8b14ef | Text | 12,911 | 268 | # DiffSBDD: Structure-based Drug Design with Equivariant Diffusion Models
Official implementation of **DiffSBDD**, an equivariant diffusion model for structure-based drug design, by Arne Schneuing, Charles Harris, Yuanqi Du, Kieran Didi, Arian Jamasb, Ilia Igashov, Weitao Du, Carla Gomes, Tom Blundell, Pietro Lio, Max... |
b20c70107800451f11b5ff1bbf99375ecb890bfc8affacf3da6b42ee3a819718 | Text | 12,965 | 155 | # CPSign REST Services
Web services for running [CPSign](https://arosbio.com/) predictive models as REST services. The models should be generated using the open source program [CPSign](https://github.com/arosbio/cpsign) - see preprint [CPSign at bioRxiv](https://www.biorxiv.org/content/10.1101/2023.11.21.568108v1).
... |
60b31a5c1fbff5b8542273bbe80c0f21bf056f429679de12756ae4914ffe64b3 | Text | 12,974 | 273 | MicrogliaMorphology
================
#### *An ImageJ macro for microglia morphology analysis*
**Created**: 15 June, 2023 **Last updated**: 7 January, 2026
## Welcome to MicrogliaMorphology!
MicrogliaMorphology is a user-friendly ImageJ macro that offers a
semi-automated approach to characterize 27 morphology featur... |
2e4b19cdbb5f072468f0e567034b3965f9e8c5f70bf30fa282e55dba1b9951bc | Text | 13,218 | 245 | # MorphyLib [](https://travis-ci.org/mbrazeau/MorphyLib) [](https://coveralls.io/github/mbrazeau/MorphyLib?branch=development) 
# AlphaFold 3
This package provides an implementation of the inference pipeline of
AlphaFold 3. See below for how to access the model parameters. You may only use
AlphaFold 3 model parameters if received directly from Google. Use is subject to
these
[terms of use](https://github.com/google-... |
603e5aef54343367aea147f5be02a7ba807a7f17b896adf51cfdf1b620c56c8e | Text | 13,268 | 245 | # MorphyLib [](https://travis-ci.org/mbrazeau/morphylib) [](https://coveralls.io/github/mbrazeau/MorphyLib?branch=development) [:
Chakrabarti, A. M., Capitanchik, C., Ule, J., & Luscombe, N. M. (2021). clipplotr-a comparative visualisation and analysis tool for CLIP data. bioRxiv.
## Table of contents
1. [About _clipplotr_](#about-cli... |
75a83924fa71c2dd251c466694e26c2ca63f7f612fc587a787ec8c6c4a1293db | Text | 13,722 | 181 | # Supplementary code repository for: A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations
Authors: Ingrid M. Saldana-Guerrero<sup>1,2,3,\*</sup>, Luis F. Montano-Gutierrez<sup>4,\*</sup>, Katy Boswell<sup>1,2,$</sup>, Christoph Hafemeister<sup>4,$</sup>, Evon ... |
c2349464821225e580d084cf11720c01fd4eccbf9262eb36b340276eb0a387c1 | Text | 14,191 | 326 | Long-read RNA sequencing identifies region- and sex-specific C57BL/6J
mouse brain mRNA isoform expression and usage
================
2023-12-13
Preprint DOI badge placeholder
## Authors
**Emma F. Jones, Timothy C. Howton, Victoria L. Flanary, Amanda D.
Clark, and Brittany N. Lasseigne.**
The University of Alabama a... |
41cf2d9a779a712e86a4c708c2601bc88ffe219b86c7f38360a368ebd52ce68f | Text | 14,561 | 298 | # SE(3) diffusion model with application to protein backbone generation
## Description
Implementation for "SE(3) diffusion model with application to protein backbone generation" [arxiv link](https://arxiv.org/abs/2302.02277).
While our work is tailored towards protein backbone generation, it is in principle applicable... |
16702b378ea6a158614be001b21fe8a420a5603141fec063edbf9c14d9ca6add | Text | 14,590 | 232 | # Bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
- This repo contains code for the paper [ChromBPNet: Bias factorized, base-resolution deep learning models of chromatin accessibility reveal ... |
64cd87abe6f097492127f70c6c33f6d95445af4a236b20c34def9c0c218e704f | Text | 14,764 | 222 | <img src='imgs/horse2zebra.gif' align="right" width=384>
<br><br><br>
# CycleGAN
### [PyTorch](https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix) | [project page](https://junyanz.github.io/CycleGAN/) | [paper](https://arxiv.org/pdf/1703.10593.pdf)
Torch implementation for learning an image-to-image translati... |
666837bb2e75f42c18cc37e811c7b11548dfb3774c4fc6173526cbae88cda5be | Text | 14,800 | 334 | Long-read RNA sequencing identifies region- and sex-specific C57BL/6J
mouse brain mRNA isoform expression and usage
================
2024-06-25
bioRxiv Preprint:
[](https://doi.org/10.1101/2024.01.11.575219)
Publishe... |
5a4307f6fbad0037a0f193a3036a8f7ffed4da4a1aaed45fe4d4d634df7418c2 | Text | 14,902 | 208 | ---
# SMdRQA: Implementing Sliding Window MdRQA to get Summary Statistics Estimate of MdRQA measures from the Data
---
**Description:**
SMdRQA is a powerful Python package designed for conducting Sliding Window Multidimensional Recurrent Quantification Analysis (SMdRQA). This specialized analysis technique allows re... |
e0db59e2c42e8a281bea2062072a8d03c88bb0facff4effc2e9bfb8c2b60ed8b | Text | 15,004 | 220 | # Pathformer
[](https://www.python.org/)
## Pathformer: a biological pathway informed Transformer for disease diagnosis and prognosis using multi-omics data
Integrating multi-omics data offers a more comprehensive view of gene regulation, which ... |
e807b9210f38a13149f05a5cd9f3873ef5c6be9fa58d135c7b681f8bd7c41823 | Text | 15,183 | 351 | .. image:: https://img.shields.io/pypi/v/TEtranscripts?logo=python
:target: https://pypi.org/project/TEtranscripts/
.. image:: https://img.shields.io/docker/v/mhammelllab/tetranscripts?logo=docker&label=docker%2Fsingularity
:target: https://hub.docker.com/r/mhammelllab/tetranscripts/tags
.. image:: https://zenodo.o... |
b4d1e717b65f84ca7e4cd31187b08b9e1bca30c6744b183e76528015fb5c0d88 | Text | 15,341 | 199 | <img align="left" width="80" height="80" src="https://raw.githubusercontent.com/LabTrivedi/MOrgAna/master/morgana/Examples/app_screenshots/morgana_icon.png" alt="morgana">
# MOrgAna
Welcome to MOrgAna (Machine-learning based Organoids Analysis) to segment and analyse 2D multi-channel images of organoids, as described... |
47573b43bc04c1de176e6c52b870e7b8fbaaf554c336f39692961a28896542a1 | Text | 15,346 | 183 | # Neural Topic Models with Survival Supervision
A neural network approach that jointly learns a survival model, which predicts time-to-event outcomes, and a topic model, which captures how features relate.
This code accompanies the paper:
> George H. Chen\*, Linhong Li\*, Ren Zuo, Amanda Coston, Jeremy C. Weiss. "Ne... |
7860e6d27339f0a35a2f8ba8e0f6ad2b43230503ab71bfb91daccf5c0000ef4e | Text | 15,390 | 236 | # Single-cell RNA-seq of a CRISPR-engineered endogenous tauopathy model
[](https://doi.org/10.5281/zenodo.22237381)
Analysis code supporting the study **“Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a *Dros... |
59cbffaf2b3dbeeec2ca3b2739840cadb627db458912d367b4ff044d91f0b0ac | Text | 15,647 | 196 | # abcd-bids-tfmri-pipeline
## Purpose
This tool is a modified version of the TaskfMRIAnalysis stage of the HCP-pipeline (Glasser et al., 2013) developed at University of Vermont by Anthony Juliano and can be used to complete Level 1 and Level 2 analyses of task fMRI dtseries data. Specifically, this tool was designed ... |
53f4b682807d9114eb241e090cc9a70bb90794a4a4a18eecaba959065c935cf2 | Text | 15,853 | 380 | ================
``langid.py`` readme
================
Introduction
------------
``langid.py`` is a standalone Language Identification (LangID) tool.
The design principles are as follows:
1. Fast
2. Pre-trained over a large number of languages (currently 97)
3. Not sensitive to domain-specific features (e.g. HTML/X... |
39bead1a176e29fdd40b6f4a737053d9f55c08fba001598be4fcc9a8b1041382 | Text | 15,952 | 208 | <img src="media/banner.png">
#### [[Project]](https://sites.google.com/view/stylegan-xl/) [[PDF]](https://arxiv.org/abs/2202.00273) [](https://huggingface.co/spaces/hysts/StyleGAN-XL)
This repository contains code fo... |
c9c30794be7e665097e4278fa5520c5676dac10d5f6c18682211957d285db640 | Text | 16,213 | 224 | GENERAL INFORMATION: General overview
-------------------------------------
1. Title of dataset:
Synergistic olfactory processing for social plasticity in desert locusts
2. Author information:
2.1. Inga Petelski
University of Konstanz
ORC... |
9cf93e61c1fbbd139678f5fe698ae36a69b952b70a67fe062ff20878231dbacc | Text | 16,261 | 428 | <div align="center">
# DDSurfer
**Cortical surface reconstruction from diffusion MRI**
[](#key-dependencies)
[](#key-dependencies)
[!... |
3e6329fa0c0cd8180026929287116e306a012a7d07ffe30daf9a381d2748fffa | Text | 16,299 | 83 | # NASA_RR3_Brain
Here, one can find the scripts used in the analysis of the mouse brain data used in the study titled "**_Spatially resolved multiomics on the neuronal effects induced by spaceflight_**"
*Impairment of the central nervous system (CNS) poses a significant health risk for astronauts during long-duration ... |
7942ee4a4d300770da67ce0b7e6c2c7e7f4ff45acdc45bd91e82153910693818 | Text | 16,306 | 227 | MIMIC-III Benchmarks
=========================
[](https://gitter.im/YerevaNN/mimic3-benchmarks?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
Python suite to construct b... |
e152fe205cf8595576ff47351c7be84e34353fc1f88cb23b2a17de58ad497859 | Text | 16,397 | 231 |
<p align="center">
<img src="smdrqa_logo.png" width="20%">
</p>
---
# SMdRQA: Implementing Sliding Window MdRQA to get Summary Statistics Estimate of MdRQA measures from the Data
---
**Description:**
SMdRQA is a powerful Python package designed for conducting Sliding Window Multidimensional Recurrent Quantificat... |
497042cf9010c683528c6df85e2a48a458e48c968a28c21dbd43b0afb82f4bb2 | Text | 16,496 | 304 | # HeteroTCR: A heterogeneous graph neural network-based method for predicting peptide-TCR interaction
[](https://zenodo.org/doi/10.5281/zenodo.11118487)
PyTorch implementation for [HeteroTCR](https://github.com/yuzilan/HeteroTCR) [[paper]](https://www.nature.com/articles/... |
e8298781e1dc2b0d261cd89728055b03d62f077611557f20f630de6cc78b61a5 | Text | 17,118 | 407 |
# SSCD
Salmon Scale Circuli Detector (SSCD)
__Table of Contents__
- [Prerequisites](#markdown-header-prerequisites)
- [Installation](#markdown-header-installation)
- [How to run SSCD](#markdown-header-how-to-run-sscd)
- [Evaluating SSCD's performance](#markdown-header-evaluating-sscds-performance)
... |
5a7fcfb8273134652dc9635ec2c3cbcb6e878b7b405a9a15039a4e4add1d3d08 | Text | 17,331 | 150 | # OpenFF Force Fields
[](https://github.com/openforcefield/openff-forcefields/actions?query=branch%3Amaster+workflow%3ACI) [](https:... |
198e3311a3a538cac678243de53b379a8bf160800d1ab8e7cdaefb971d83bc9e | Text | 17,398 | 242 | <p align="center">
<img src="docs/fairseq_logo.png" width="150">
<br />
<br />
<a href="https://opensource.fb.com/support-ukraine"><img alt="Support Ukraine" src="https://img.shields.io/badge/Support-Ukraine-FFD500?style=flat&labelColor=005BBB" /></a>
<a href="https://github.com/pytorch/fairseq/blob/main/LICE... |
91d43ebe7c0b5b1fa0cc326b785d215a560a92bb724d6ee03d9681a3d462f775 | Text | 18,063 | 255 | <img src="assets/chroma_logo_outline.svg" width="280">
[**Get Started**](#get-started)
| [**Sampling**](#sampling)
| [**Design**](#design)
| [**Conditioners**](#conditioners)
| [**License**](#license)
Chroma is a generative model for designing proteins **programmatically**.
Protein space is complex and hard to navig... |
ab96b3572afa7c7bf52ba5c15892f9b49879b3844e60e87b8003f005d4c8a9bf | Text | 18,554 | 424 | # Predmoter
Predict promoter and enhancer associated next generation sequencing (NGS) data,
Assay for Transposase Accessible Chromatin using sequencing (ATAC-seq) and
histone (H3K4me3) Chromatin immunoprecipitation DNA-sequencing (ChIP-seq),
base-wise for plant species.
Pretrained models can be found at: htt... |
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